[main_samview] fail to read the header from "-"

[kishor2019]

Bash script:

Set input and parameters

round=2 threads=20 read1=/mnt/disk2/Lab_Users/KISHOR/mnspt4/tenili_reseq_50x/X101SC23121795-Z01-J001/00.CleanData/3157_3/3157_3_1.clean.fq.gz read2=/mnt/disk2/Lab_Users/KISHOR/mnspt4/tenili_reseq_50x/X101SC23121795-Z01-J001/00.CleanData/3157_3/3157_3_2.clean.fq.gz input=/mnt/disk2/Lab_Users/KISHOR/mnspt4/assembly_annotation/NECAT/manual/tenili.fa for ((i=1; i<=${round};i++)); do

step 1:

index the genome file and do alignment

bwa index ${input}; bwa mem -t ${threads} ${input} ${read1} ${read2}|samtools view --threads 3 -F 0x4 -b -|samtools fixmate -m --threads 3 - -|samtools sort -m 2g --threads 5 -|samtools markdup --threads 5 -r - sgs.sort.bam

index bam and genome files

samtools index -@ ${threads} sgs.sort.bam; samtools faidx ${input}; (base)[room@black01 manual]$ python /mnt/genome3/Lab_Users/Kishor/DISK_2/softwares/NextPolish/lib/nextpolish1.py -g ${input} -t 1 -p ${threads} -s sgs.sort.bam > tenili.polishtemp.fa; input=tenili.polishtemp.fa;

step2:

index genome file and do alignment

bwa index ${input}; bwa mem -t ${threads} ${input} ${read1} ${read2}|samtools view --threads 3 -F 0x4 -b -|samtools fixmate -m --threads 3 - -|samtools sort -m 2g --threads 5 -|samtools markdup --threads 5 -r - sgs.sort.bam

index bam and genome files

samtools index -@ ${threads} sgs.sort.bam; samtools faidx ${input};

polish genome file

pythonn /mnt/genome3/Lab_Users/Kishor/DISK_2/softwares/NextPolish/lib/nextpolish1.py -g ${input} -t 2 -p ${threads} -s sgs.sort.bam > tenili.nextpolish.fa; input=tenili.nextpolish.fa; done;

Finally polished genome file: tenili.nextpolish.fa

Error text:

[main_samview] fail to read the header from "-". [bam_mating_core] ERROR: Couldn't read header samtools sort: failed to read header from "-" [markdup] error reading header samtools index: "sgs.sort.bam" is in a format that cannot be usefully indexed [faidx] Could not build fai index tenili.polishtemp.fa.fai

Can i have please have any help to solve this issue?

[moold]

I think you can try to update samtools to the lastest version.